300
phototrophic anaerobe, Rhodospirillum photometricum. For
chloroethenes and chlorinated aromatics, their mineraliza-
tion into CO 2 and Cl− was essentially observed in mixed cul-
tures under methanogenic, iron-reducing, humus-reducing
and manganese-reducing conditions (for review see Field
and Sierra-Alvarez 2004 ). Moreover, in previous studies
Thauera chlorobenzoica strain 3CB-1 was reported to utilize
3-chlorobenzoate as sole sources of cell carbon and energy
growth substrate under denitrifying conditions (Song et al.
2001 ; Kuntze et al. 2011 ).
Reductive Dehalogenation Through Organohalide
Respiration
Organohalide respiration (OHR) is the more efficient and the
well-studied biodegradation pathway of chlorinated com-
pounds under anaerobic conditions. In this respiratory pro-
cess, bacteria use chlorinated species as the terminal electron
acceptors during electron-based energy conservation
(Holliger et al. 1998b). Highly reduced anaerobic environ-
ments (indicated by a low redox potential), typical for meth-
anogenesis and sulfate-reduction, have been found to be a
requisite for the reductive dechlorination of halogenated
compounds (i.e., the substitution of halogen atoms by hydro-
gen atoms) (Stuart et al. 1999 ; Olivas et al. 2002 ). Almost all
chlorinated compounds, whatever the molecular structure
and the number of substitutions, can be degraded through
this microbial process.
OHR is performed by organohalide-respiring bacteria
(OHRBs) that have been identified in various taxa including
the δ-Proteobacteria, ε-Proteobacteria, Firmicutes and
Chloroflexi. These bacteria are divided into two categories,
i.e. facultative and obligate OHRBs. Besides Clorg, faculta-
tive OHRBs are able to use a wide diversity of electron
acceptors (e.g. fumarate, nitrate, sulfate, thiosulfate, Fe(III),
Mn(IV), U(VI), S^0 , selenate, arsenate) but also several elec-
tron donors (H 2 , pyruvate, acetate, lactate, butyrate, succi-
nate, formate, ethanol, glycerol, crotonate). They include
members of the Desulfomonile, Geobacter, Sulfurospirillum
and Desulfitobacterium genera (Bradley and Chapelle 2000 ;
Smidt and de Vos 2004 ; Hiraishi 2008 ). The second category
of ORHBs, and possibly the most intriguing, is composed of
extremely specialized bacteria requiring an organohalide
molecule as terminal electron acceptor, H 2 or acetate as elec-
tron donor and vitamin B12 as cofactor to perform
OHR. Currently, obligate OHRBs are present in the
Chloroflexi phylum with representatives of the
“Dehalococcoidia” class such as Dehalococcoides and
Dehalogenimonas species (Löffler et al. 2013 ) and in the
Firmicutes, within the Dehalobacter genus (Holliger et al.
1998a).
OHR reactions are catalyzed by the reductive dehaloge-
nases (RDase), an iron-sulfur and corrinoid containing fam-
ily of enzymes, which is very diverse and whose number is
continually growing, suggesting that the diversity of this pro-
tein family is much deeper than is currently accounted for
(Hug and Edwards 2013 ). Reductive dehalogenase genes
typically comprise an operon containing rdhA (gene for cata-
lytically active enzyme), rdhB (gene for a putative membrane-
anchoring protein) and sometimes one or more associated
genes (rdhTKZECD) (Smidt et al. 2000 ). The rdhA genes
have been identified in a wide variety of strictly anaerobic
microorganisms, in which a unique archaeal Ferroglobus
species (Hug and Edwards 2013 ; Hug et al. 2013 ). Genomic
analysis and genome comparisons between obligate and fac-
ultative OHRBs recently revealed specific features such as
the presence of multiple putative RDase genes (up to 39) in
the genome of obligate OHRBs. These genes are generally
localized in high plasticity regions suggesting an important
role of gene transfer and/or genomic rearrangement in the
adaptation of these microorganisms (Kube et al. 2005 ;
McMurdie et al. 2009 ; Kruse et al. 2013 ; Richardson 2013 ).Dehalogenation by Anaerobic Co-metabolism
Anaerobic co-metabolism results in the partial or complete
reductive dehalogenation of chlorinated compounds. This
kind of metabolism has been shown for a wide variety of
lightly and heavily chlorinated aliphatics while it is more
rarely shown for chlorinated aromatics (for review see Field
and Sierra-Alvarez 2004 ). Regarding aliphatics, the majority
of studies reveal that they can be slowly co-metabolized by
pure or mixed cultures involving mainly methanogens but
also acetogenic, fermentative, sulfate-reducing and iron-
reducing bacteria. Rapid anaerobic co-metabolism was
observed in a few cases (e.g. pentachloroethane, chloroeth-
enes) due to an enzymatic reduction by a reductive dehaloge-
nase expressed for another chlorinated compound. However,
the more common, slow anaerobic co-metabolism results
from the direct reaction of the chlorinated compound with
commonly occurring reduced enzyme cofactors (e.g. vitamin
B12, a common cofactor of strict anaerobes, especially those
involved in chlorine metabolism, or yet the nickel containing
coenzyme F430 of methanogens). Regarding aromatic com-
pounds, anaerobic co-metabolism degradation has essen-
tially been observed for chlorobenzenes and PCBs. For the
formers, best examples are tetrachlorobenzene and hexa-
chlorobenzene dehalogenation by Staphylococcus epidermi-
dis (Tsuchiya and Yamaha 1984 ) but also in anaerobic
sewage sludge respectively (Yuan et al. 1999 ). About PCBs,
only a few congeners were demonstrated to be subject to co-
metabolic reductive dechlorination as long as more highly
chlorinated parent compounds were present in the non-
methanogenic mixed culture (May et al. 2006 ).
Methanogenesis is a very active process in Lake Pavin.
Although CH 4 production has been demonstrated in the
anoxic water layers, CH 4 concentration is mainly due to CH 4
flux from the sediment. More details on methane cycle andE. Dugat-Bony et al.